7E7D

Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VXX 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.092
f_angle_d0.845
f_chiral_restr0.058
f_bond_d0.008
f_plane_restr0.006
Sample
SARS-CoV-2 spike protein fused to the C-terminal region of human type 1a collagen
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK I
Cryogen NameETHANE
Sample Vitrification Detailsblot time 2 seconds, blot force 4, waiting time 8 seconds
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles173288
Reported Resolution (Å)3.2
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (6VXX)
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)50
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification64000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
CTF CORRECTIONCTFFIND4
MODEL FITTINGCoot0.9-pre
MODEL REFINEMENTPHENIX1.16-3549
CLASSIFICATIONRELION3.0.7
RECONSTRUCTIONRELION3.0.7
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION1504770